The bones and cartilages of the jaws, face, neck, and inner ear develop from migratory precursors called neural crest cells (NCCs). In the ventral portion of the embryonic head, NCCs populate structures called the pharyngeal arches. The pharyngeal arches control multiple aspects of NCC development, including their migration, patterning, and differentiation. Consistent with this, mutations in genes involved in pharyngeal arch formation underlie the craniofacial defects of DiGeorge (Tbx1) and Bamforth-Lazarus (Foxe1) syndromes. Similar skeletal abnormalities have been linked to in utero disruption of retinoic acid (RA) signaling, an essential regulator of pharyngeal arch formation. Understanding the complex genetic and molecular interactions underlying pharyngeal arch development is the first step toward identifying the causes of, and treatments for, genetic and environmentally-induced disruptions of head skeleton development. Morphologically, pharyngeal arch development begins with out-pocketings of endoderm called the pharyngeal pouches. The lateral outgrowth of the pouches, and their fusion with overlying ectoderm, partitions the walls of the pharynx, creating the pharyngeal arches. A few of the genes driving pharyngeal pouch initiation and outgrowth have been identified, including the transcription factors Tbx1/10 and Pax1/9. These factors are coexpressed with several other transcriptional regulators and signaling molecules in the pharyngeal endoderm. The evolutionarily conserved expression and function of these genes suggest they are part of a gene regulatory network (GRN) for pouch formation. However, the precise regulatory relationships between these putative pouch GRN components and how their segmental expression is first established in the pharyngeal endoderm, is unknown. The proposed work will address these gaps in our knowledge using an innovative comparative approach incorporating the sea lamprey Petromyzon marinus and the frog Xenopus laevis. The sea lamprey is the most basal vertebrate amenable to developmental manipulations. Due to its slow development, morphologically simple pharyngeal apparatus, and large number of similar pharyngeal pouches, the sea lamprey is particularly well-suited to studying the dynamic, iterated genetic interacts driving pouch formation. Furthermore, technical advances have made genetic manipulations in this species routine. Comparisons of gene expression and function between lamprey and X. laevis, a tetrapod vertebrate, will highlight the core, conserved aspects of the pharyngeal pouch GRN likely operating in all vertebrates, including humans. The specific aims of the work are to address these 4 questions: 1) what are the positions of Six1, Eya, and Foxq1 in the pharyngeal pouch GRN?; 2) do segmental Wnt11r and FGF8 signals from adjacent tissues activate expression of pouch GRN components in the pharyngeal endoderm?; 3) does a RA signaling gradient form a differentiation `wavefront' that regulates iterated activation of pouch GRN components? and 4) does a `clock' of oscillating gene expression establish segmental expression of pouch GRN components?